Solvation structure and hydrogen bond dynamics of uracil–water and thymine–water: A comparison of different force fields of uracil and thymine
Published:21 May 2024
DOI: 10.1016/j.cplett.2024.141357
Chinmay Parida, Snehasis Chowdhuri
Abstract
Molecular dynamics simulations of uracil and thymine are carried out at 308?K to investigate the hydrogen bonding structures and dynamics in an aqueous solution. Thymine shows higher hydrogen-bond interactions with water molecules compared to uracil for all the models compared here. The dipole rotation of thymine in water is significantly slower compared to uracil. Water–water hydrogen bond lifetime is higher compared to uracil/thymine–water hydrogen bonds. Karplus and Kollman models of thymine show higher solvation free energy (SFE). The SFE of uracil for Karplus and Kollman model is closer to the experimentally reported value (–16.06?kcal/mol) at 298?K.